chr11-48360919-A-G

Variant names:

• chr11-48360919-A-G
• rs1351696

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.817 in 152,076 control chromosomes in the GnomAD database, including 51,264 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.82 (51264 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.767
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124163 AN: 151958 Hom.: 51215 Cov.: 32

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.859

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.817 AC: 124268 AN: 152076 Hom.: 51264 Cov.: 32 AF XY: 0.816 AC XY: 60653 AN XY: 74346

African (AFR) AF: 0.707 AC: 29301 AN: 41464

American (AMR) AF: 0.866 AC: 13230 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.891 AC: 3092 AN: 3472

East Asian (EAS) AF: 0.834 AC: 4321 AN: 5178

South Asian (SAS) AF: 0.862 AC: 4158 AN: 4824

European-Finnish (FIN) AF: 0.825 AC: 8706 AN: 10556

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.862 AC: 58571 AN: 67984

Other (OTH) AF: 0.862 AC: 1820 AN: 2112

Alfa AF: 0.845 Hom.: 61377

Bravo AF: 0.816

Asia WGS AF: 0.862 AC: 2999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.51
PhyloP100		-0.77

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1351696; hg19: chr11-48382471;